The Blue Obelisk mailing list has seen an interesting discussion on ambiguity in the term ‘open source’, triggered by a study by Beth Ritter Guth. For example, Jean-Claude Bradley performs ‘open source’ science (see his Useful Chemistry blog) who is not opposed to using closed source software, while the Blue Obelisk is about ‘open source’ software.

Google has set up a new search enginge specifically for source code: /* Code Search */. Important difference with their normal search engine is that it allows restricting your search by programming language, license and filename and package. I have not been able to figure out how to use ‘package’ yet, but the others are pretty clear.

I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.

Bernard Munos at Eli Lilly & Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&D reinvigorate drug research?

Joerg Wegner mentioned in his blog the graph mining program ParMol which integrates four mining algorithms: MoSS (aka MoFa) and Gaston, which I mentioned in November last year , and FFSM and gSpan, which I did not know about yet. ParMol provides a common interface to the four different algorithms and is, like the four mining modules, licensed GPL.

Rajarshi Guha has set a nightly build service for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.